src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.schemes.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.analysis.*;\r
  25 import jalview.io.*;\r
  26 import java.awt.*;\r
  27 import java.awt.event.*;\r
  28 import java.util.*;\r
  29 import java.io.InputStreamReader;\r
  30 import java.io.BufferedReader;\r
  31 import java.net.URL;\r
  32 \r
  33 \r
  34 public class AlignFrame extends Frame implements ActionListener,\r
  35     ItemListener, KeyListener, MouseListener\r
  36 {\r
  37   public AlignmentPanel alignPanel;\r
  38   public AlignViewport viewport;\r
  39   int NEW_WINDOW_WIDTH = 700;\r
  40   int NEW_WINDOW_HEIGHT = 500;\r
  41   jalview.bin.JalviewLite applet;\r
  42 \r
  43 \r
  44   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
  45   {\r
  46     try{\r
  47       jbInit();\r
  48     }catch(Exception ex)\r
  49     {\r
  50       ex.printStackTrace();\r
  51     }\r
  52 \r
  53     this.applet = applet;\r
  54     viewport = new AlignViewport(al, applet);\r
  55     alignPanel = new AlignmentPanel(this, viewport);\r
  56 \r
  57     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  58 \r
  59     if(applet!=null)\r
  60     {\r
  61       String param = applet.getParameter("sortBy");\r
  62       if (param != null)\r
  63       {\r
  64         if (param.equalsIgnoreCase("Id"))\r
  65           sortIDMenuItem_actionPerformed();\r
  66         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  67           sortPairwiseMenuItem_actionPerformed();\r
  68       }\r
  69 \r
  70       param = applet.getParameter("wrap");\r
  71       if (param != null)\r
  72       {\r
  73         if (param.equalsIgnoreCase("true"))\r
  74         {\r
  75           wrapMenuItem.setState(true);\r
  76           wrapMenuItem_actionPerformed();\r
  77         }\r
  78       }\r
  79 \r
  80       try\r
  81       {\r
  82         param = applet.getParameter("windowWidth");\r
  83         if (param != null)\r
  84         {\r
  85           int width = Integer.parseInt(param);\r
  86           NEW_WINDOW_WIDTH = width;\r
  87         }\r
  88         param = applet.getParameter("windowHeight");\r
  89         if (param != null)\r
  90         {\r
  91           int height = Integer.parseInt(param);\r
  92           NEW_WINDOW_HEIGHT = height;\r
  93         }\r
  94       }\r
  95       catch (Exception ex)\r
  96       {}\r
  97 \r
  98     }\r
  99 \r
 100    //Some JVMS send keyevents to Top frame or lowest panel,\r
 101    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 102    this.addKeyListener(this);\r
 103    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 104    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 105 \r
 106     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 107     {\r
 108      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 109      {\r
 110        if (evt.getPropertyName().equals("alignment"))\r
 111        {\r
 112          alignmentChanged();\r
 113        }\r
 114      }\r
 115    });\r
 116 \r
 117 \r
 118    add(alignPanel, BorderLayout.CENTER);\r
 119    jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 120 \r
 121    alignPanel.validate();\r
 122    alignPanel.repaint();\r
 123   }\r
 124   public AlignViewport getAlignViewport()\r
 125   {\r
 126     return viewport;\r
 127   }\r
 128 \r
 129   public SeqCanvas getSeqcanvas()\r
 130   {\r
 131     return alignPanel.seqPanel.seqCanvas;\r
 132   }\r
 133 \r
 134 \r
 135   /**\r
 136    * DOCUMENT ME!\r
 137    *\r
 138    * @param String DOCUMENT ME!\r
 139    */\r
 140 \r
 141   public void parseFeaturesFile(String file)\r
 142   {\r
 143     try\r
 144     {\r
 145       URL url = new URL(file);\r
 146 \r
 147       BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));\r
 148       SequenceI seq = null;\r
 149       String line, type, desc, token;\r
 150 \r
 151       int index, start, end;\r
 152       StringTokenizer st;\r
 153       SequenceFeature sf;\r
 154       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
 155       int lineNo = 0;\r
 156       while ( (line = in.readLine()) != null)\r
 157       {\r
 158         lineNo++;\r
 159         st = new StringTokenizer(line, "\t");\r
 160         if (st.countTokens() == 2)\r
 161         {\r
 162           type = st.nextToken();\r
 163           UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 164           fr.setColour(type, ucs.findColour("A"));\r
 165           continue;\r
 166         }\r
 167 \r
 168         while (st.hasMoreElements())\r
 169         {\r
 170           desc = st.nextToken();\r
 171           token = st.nextToken();\r
 172           if (!token.equals("ID_NOT_SPECIFIED"))\r
 173           {\r
 174             index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 175                 token));\r
 176             st.nextToken();\r
 177           }\r
 178           else\r
 179           {\r
 180             index = Integer.parseInt(st.nextToken());\r
 181           }\r
 182 \r
 183           start = Integer.parseInt(st.nextToken());\r
 184           end = Integer.parseInt(st.nextToken());\r
 185 \r
 186           seq = viewport.alignment.getSequenceAt(index);\r
 187 \r
 188           type = st.nextToken();\r
 189 \r
 190           if(fr.getColour(type)==null)\r
 191           {\r
 192             // Probably the old style groups file\r
 193             UserColourScheme ucs = new UserColourScheme(type);\r
 194             fr.setColour(type, ucs.findColour("A"));\r
 195           }\r
 196 \r
 197           sf = new SequenceFeature(type, desc, "", start, end);\r
 198 \r
 199           seq.addSequenceFeature(sf);\r
 200         }\r
 201       }\r
 202 \r
 203       viewport.showSequenceFeatures = true;\r
 204       viewMenu.addSeparator();\r
 205       viewMenu.add(sequenceFeatures);\r
 206       viewMenu.add(featureSettings);\r
 207 \r
 208 \r
 209       alignPanel.repaint();\r
 210 \r
 211     }\r
 212     catch (Exception ex)\r
 213     {\r
 214       ex.printStackTrace();\r
 215       System.out.println("Error parsing groups file: " + ex);\r
 216     }\r
 217   }\r
 218 \r
 219   public void keyPressed(KeyEvent evt)\r
 220   {\r
 221     switch (evt.getKeyCode())\r
 222     {\r
 223       case 27: // escape key\r
 224         deselectAllSequenceMenuItem_actionPerformed();\r
 225         break;\r
 226       case KeyEvent.VK_X:\r
 227         if (evt.isControlDown() || evt.isMetaDown())\r
 228         {\r
 229           cut_actionPerformed();\r
 230         }\r
 231         break;\r
 232       case KeyEvent.VK_C:\r
 233         if (evt.isControlDown() || evt.isMetaDown())\r
 234         {\r
 235           copy_actionPerformed();\r
 236         }\r
 237         break;\r
 238       case KeyEvent.VK_V:\r
 239         if (evt.isControlDown() || evt.isMetaDown())\r
 240         {\r
 241           paste(true);\r
 242         }\r
 243         break;\r
 244       case KeyEvent.VK_A:\r
 245         if (evt.isControlDown() || evt.isMetaDown())\r
 246         {\r
 247           selectAllSequenceMenuItem_actionPerformed();\r
 248         }\r
 249         break;\r
 250       case KeyEvent.VK_DOWN:\r
 251         moveSelectedSequences(false);\r
 252         break;\r
 253       case KeyEvent.VK_UP:\r
 254         moveSelectedSequences(true);\r
 255         break;\r
 256       case KeyEvent.VK_F:\r
 257         if (evt.isControlDown())\r
 258         {\r
 259           findMenuItem_actionPerformed();\r
 260         }\r
 261         break;\r
 262       case KeyEvent.VK_BACK_SPACE:\r
 263       case KeyEvent.VK_DELETE:\r
 264         cut_actionPerformed();\r
 265         break;\r
 266     }\r
 267   }\r
 268   public void keyReleased(KeyEvent evt)\r
 269   {}\r
 270   public void keyTyped(KeyEvent evt)\r
 271   {}\r
 272 \r
 273 public void itemStateChanged(ItemEvent evt)\r
 274   {\r
 275     if(evt.getSource()==colourTextMenuItem)\r
 276             colourTextMenuItem_actionPerformed();\r
 277     else if(evt.getSource()==wrapMenuItem)\r
 278             wrapMenuItem_actionPerformed();\r
 279     else if(evt.getSource()==scaleAbove)\r
 280             scaleAbove_actionPerformed();\r
 281     else if(evt.getSource()==scaleLeft)\r
 282             scaleLeft_actionPerformed();\r
 283     else if(evt.getSource()==scaleRight)\r
 284             scaleRight_actionPerformed();\r
 285      else if(evt.getSource()==seqLimits)\r
 286       seqLimits_itemStateChanged();\r
 287     else if(evt.getSource()==viewBoxesMenuItem)\r
 288             viewBoxesMenuItem_actionPerformed();\r
 289     else if(evt.getSource()==viewTextMenuItem)\r
 290             viewTextMenuItem_actionPerformed();\r
 291     else if(evt.getSource()==renderGapsMenuItem)\r
 292             renderGapsMenuItem_actionPerformed();\r
 293     else if(evt.getSource()==annotationPanelMenuItem)\r
 294             annotationPanelMenuItem_actionPerformed();\r
 295       else if(evt.getSource()==sequenceFeatures)\r
 296        {     viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 297             alignPanel.seqPanel.seqCanvas.repaint();\r
 298         }\r
 299       else if(evt.getSource()==conservationMenuItem)\r
 300             conservationMenuItem_actionPerformed();\r
 301       else if(evt.getSource()==abovePIDThreshold)\r
 302             abovePIDThreshold_actionPerformed();\r
 303           else if(evt.getSource()==applyToAllGroups)\r
 304             applyToAllGroups_actionPerformed();\r
 305   }\r
 306  public void actionPerformed(ActionEvent evt)\r
 307  {\r
 308     if(evt.getSource()==inputText)\r
 309       inputText_actionPerformed();\r
 310     else if(evt.getSource()==closeMenuItem)\r
 311       closeMenuItem_actionPerformed();\r
 312     else if(evt.getSource()==copy)\r
 313       copy_actionPerformed();\r
 314     else if(evt.getSource()==undoMenuItem)\r
 315       undoMenuItem_actionPerformed();\r
 316     else if(evt.getSource()==redoMenuItem)\r
 317       redoMenuItem_actionPerformed();\r
 318     else if(evt.getSource()==inputText)\r
 319             inputText_actionPerformed();\r
 320     else if(evt.getSource()==closeMenuItem)\r
 321             closeMenuItem_actionPerformed();\r
 322     else if(evt.getSource()==undoMenuItem)\r
 323             undoMenuItem_actionPerformed();\r
 324     else if(evt.getSource()==redoMenuItem)\r
 325             redoMenuItem_actionPerformed();\r
 326     else if(evt.getSource()==copy)\r
 327             copy_actionPerformed();\r
 328     else if(evt.getSource()==pasteNew)\r
 329             pasteNew_actionPerformed();\r
 330     else if(evt.getSource()==pasteThis)\r
 331             pasteThis_actionPerformed();\r
 332     else if(evt.getSource()==cut)\r
 333             cut_actionPerformed();\r
 334     else if(evt.getSource()==delete)\r
 335             delete_actionPerformed();\r
 336     else if(evt.getSource()==deleteGroups)\r
 337             deleteGroups_actionPerformed();\r
 338     else if(evt.getSource()==selectAllSequenceMenuItem)\r
 339             selectAllSequenceMenuItem_actionPerformed();\r
 340     else if(evt.getSource()==deselectAllSequenceMenuItem)\r
 341             deselectAllSequenceMenuItem_actionPerformed();\r
 342     else if(evt.getSource()==invertSequenceMenuItem)\r
 343             invertSequenceMenuItem_actionPerformed();\r
 344     else if(evt.getSource()==remove2LeftMenuItem)\r
 345             remove2LeftMenuItem_actionPerformed();\r
 346     else if(evt.getSource()==remove2RightMenuItem)\r
 347             remove2RightMenuItem_actionPerformed();\r
 348     else if(evt.getSource()==removeGappedColumnMenuItem)\r
 349             removeGappedColumnMenuItem_actionPerformed();\r
 350     else if(evt.getSource()==removeAllGapsMenuItem)\r
 351             removeAllGapsMenuItem_actionPerformed();\r
 352     else if(evt.getSource()==findMenuItem)\r
 353             findMenuItem_actionPerformed();\r
 354     else if(evt.getSource()==font)\r
 355             font_actionPerformed();\r
 356     else if(evt.getSource()==featureSettings)\r
 357             featureSettings_actionPerformed();\r
 358     else if(evt.getSource()==overviewMenuItem)\r
 359             overviewMenuItem_actionPerformed();\r
 360     else if(evt.getSource()==noColourmenuItem)\r
 361             noColourmenuItem_actionPerformed();\r
 362     else if(evt.getSource()==clustalColour)\r
 363             clustalColour_actionPerformed();\r
 364     else if(evt.getSource()==zappoColour)\r
 365             zappoColour_actionPerformed();\r
 366     else if(evt.getSource()==taylorColour)\r
 367             taylorColour_actionPerformed();\r
 368     else if(evt.getSource()==hydrophobicityColour)\r
 369             hydrophobicityColour_actionPerformed();\r
 370     else if(evt.getSource()==helixColour)\r
 371             helixColour_actionPerformed();\r
 372     else if(evt.getSource()==strandColour)\r
 373             strandColour_actionPerformed();\r
 374     else if(evt.getSource()==turnColour)\r
 375             turnColour_actionPerformed();\r
 376     else if(evt.getSource()==buriedColour)\r
 377             buriedColour_actionPerformed();\r
 378     else if(evt.getSource()==nucleotideColour)\r
 379             nucleotideColour_actionPerformed();\r
 380     else if(evt.getSource()==modifyPID)\r
 381             modifyPID_actionPerformed();\r
 382     else if(evt.getSource()==modifyConservation)\r
 383             modifyConservation_actionPerformed();\r
 384     else if(evt.getSource()==userDefinedColour)\r
 385             userDefinedColour_actionPerformed();\r
 386     else if(evt.getSource()==PIDColour)\r
 387             PIDColour_actionPerformed();\r
 388     else if(evt.getSource()==BLOSUM62Colour)\r
 389             BLOSUM62Colour_actionPerformed();\r
 390     else if(evt.getSource()==sortPairwiseMenuItem)\r
 391             sortPairwiseMenuItem_actionPerformed();\r
 392     else if(evt.getSource()==sortIDMenuItem)\r
 393             sortIDMenuItem_actionPerformed();\r
 394     else if(evt.getSource()==sortGroupMenuItem)\r
 395             sortGroupMenuItem_actionPerformed();\r
 396     else if(evt.getSource()==removeRedundancyMenuItem)\r
 397             removeRedundancyMenuItem_actionPerformed();\r
 398     else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
 399             pairwiseAlignmentMenuItem_actionPerformed();\r
 400     else if(evt.getSource()==PCAMenuItem)\r
 401             PCAMenuItem_actionPerformed();\r
 402     else if(evt.getSource()==averageDistanceTreeMenuItem)\r
 403             averageDistanceTreeMenuItem_actionPerformed();\r
 404     else if(evt.getSource()==neighbourTreeMenuItem)\r
 405             neighbourTreeMenuItem_actionPerformed();\r
 406     else if(evt.getSource()==njTreeBlosumMenuItem)\r
 407             njTreeBlosumMenuItem_actionPerformed();\r
 408     else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
 409             avTreeBlosumMenuItem_actionPerformed();\r
 410     else if(evt.getSource()==documentation)\r
 411             documentation_actionPerformed();\r
 412     else if(evt.getSource()==about)\r
 413             about_actionPerformed();\r
 414 \r
 415  }\r
 416 \r
 417   public void inputText_actionPerformed()\r
 418   {\r
 419     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 420     Frame frame = new Frame();\r
 421     frame.add(cap);\r
 422     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 423   }\r
 424 \r
 425   protected void outputText_actionPerformed(ActionEvent e)\r
 426   {\r
 427     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 428     Frame frame = new Frame();\r
 429     frame.add(cap);\r
 430     jalview.bin.JalviewLite.addFrame(frame,\r
 431                                      "Alignment output - " + e.getActionCommand(),\r
 432                                      600, 500);\r
 433     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 434                                               viewport.getAlignment().getSequences(),\r
 435                                                       viewport.showJVSuffix));\r
 436   }\r
 437 \r
 438   public void closeMenuItem_actionPerformed()\r
 439   {\r
 440     PaintRefresher.components.remove(viewport.alignment);\r
 441     if(PaintRefresher.components.size()==0 && applet==null)\r
 442       System.exit(0);\r
 443 \r
 444     this.dispose();\r
 445   }\r
 446 \r
 447   Stack historyList = new Stack();\r
 448   Stack redoList = new Stack();\r
 449 \r
 450   void updateEditMenuBar()\r
 451   {\r
 452     if (historyList.size() > 0)\r
 453     {\r
 454       undoMenuItem.setEnabled(true);\r
 455       HistoryItem hi = (HistoryItem) historyList.peek();\r
 456       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 457     }\r
 458     else\r
 459     {\r
 460       undoMenuItem.setEnabled(false);\r
 461       undoMenuItem.setLabel("Undo");\r
 462     }\r
 463 \r
 464     if (redoList.size() > 0)\r
 465     {\r
 466       redoMenuItem.setEnabled(true);\r
 467       HistoryItem hi = (HistoryItem) redoList.peek();\r
 468       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 469     }\r
 470     else\r
 471     {\r
 472       redoMenuItem.setEnabled(false);\r
 473       redoMenuItem.setLabel("Redo");\r
 474     }\r
 475   }\r
 476 \r
 477   public void addHistoryItem(HistoryItem hi)\r
 478   {\r
 479     historyList.push(hi);\r
 480     updateEditMenuBar();\r
 481   }\r
 482 \r
 483   protected void undoMenuItem_actionPerformed()\r
 484   {\r
 485     HistoryItem hi = (HistoryItem) historyList.pop();\r
 486     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 487                                   HistoryItem.HIDE));\r
 488     restoreHistoryItem(hi);\r
 489     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 490   }\r
 491 \r
 492   protected void redoMenuItem_actionPerformed()\r
 493   {\r
 494     HistoryItem hi = (HistoryItem) redoList.pop();\r
 495     restoreHistoryItem(hi);\r
 496     updateEditMenuBar();\r
 497     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 498   }\r
 499 \r
 500   // used by undo and redo\r
 501   void restoreHistoryItem(HistoryItem hi)\r
 502   {\r
 503     if (hi.getType() == HistoryItem.SORT)\r
 504     {\r
 505       for (int i = 0; i < hi.getSequences().size(); i++)\r
 506       {\r
 507         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 508             elementAt(i), i);\r
 509       }\r
 510     }\r
 511     else\r
 512     {\r
 513       for (int i = 0; i < hi.getSequences().size(); i++)\r
 514       {\r
 515         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 516         if (restore.getLength() == 0)\r
 517         {\r
 518           // log.System.out.println(hi.getHidden().elementAt(i));\r
 519           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 520           viewport.alignment.getSequences().insertElementAt(\r
 521               restore,\r
 522               hi.getAlignIndex(i));\r
 523         }\r
 524         else\r
 525         {\r
 526           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 527         }\r
 528       }\r
 529       if (hi.getType() == HistoryItem.PASTE)\r
 530       {\r
 531         for (int i = viewport.alignment.getHeight() - 1;\r
 532              i > hi.getSequences().size() - 1; i--)\r
 533         {\r
 534           viewport.alignment.deleteSequence(i);\r
 535         }\r
 536       }\r
 537     }\r
 538 \r
 539     updateEditMenuBar();\r
 540 \r
 541     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 542   }\r
 543 \r
 544   public void moveSelectedSequences(boolean up)\r
 545   {\r
 546     SequenceGroup sg = viewport.getSelectionGroup();\r
 547     if (sg == null)\r
 548     {\r
 549       return;\r
 550     }\r
 551 \r
 552     if (up)\r
 553     {\r
 554       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 555       {\r
 556         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 557         if (!sg.sequences.contains(seq))\r
 558         {\r
 559           continue;\r
 560         }\r
 561 \r
 562         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 563         if (sg.sequences.contains(temp))\r
 564         {\r
 565           continue;\r
 566         }\r
 567 \r
 568         viewport.alignment.getSequences().setElementAt(temp, i);\r
 569         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 570       }\r
 571     }\r
 572     else\r
 573     {\r
 574       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 575       {\r
 576         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 577         if (!sg.sequences.contains(seq))\r
 578         {\r
 579           continue;\r
 580         }\r
 581 \r
 582         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 583         if (sg.sequences.contains(temp))\r
 584         {\r
 585           continue;\r
 586         }\r
 587 \r
 588         viewport.alignment.getSequences().setElementAt(temp, i);\r
 589         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 590       }\r
 591     }\r
 592 \r
 593     alignPanel.repaint();\r
 594   }\r
 595 \r
 596   StringBuffer copiedSequences;\r
 597   protected void copy_actionPerformed()\r
 598   {\r
 599     if (viewport.getSelectionGroup() == null)\r
 600     {\r
 601       return;\r
 602     }\r
 603 \r
 604     SequenceGroup sg = viewport.getSelectionGroup();\r
 605     copiedSequences = new StringBuffer();\r
 606     Hashtable orderedSeqs = new Hashtable();\r
 607     for (int i = 0; i < sg.getSize(); i++)\r
 608     {\r
 609       SequenceI seq = sg.getSequenceAt(i);\r
 610       int index = viewport.alignment.findIndex(seq);\r
 611       orderedSeqs.put(index + "", seq);\r
 612     }\r
 613 \r
 614     int index = 0, startRes, endRes;\r
 615     char ch;\r
 616 \r
 617     for (int i = 0; i < sg.getSize(); i++)\r
 618     {\r
 619         SequenceI seq = null;\r
 620 \r
 621         while (seq == null)\r
 622         {\r
 623             if (orderedSeqs.containsKey(index + ""))\r
 624             {\r
 625                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 626                 index++;\r
 627 \r
 628                 break;\r
 629             }\r
 630             else\r
 631             {\r
 632                 index++;\r
 633             }\r
 634         }\r
 635 \r
 636         //FIND START RES\r
 637         //Returns residue following index if gap\r
 638         startRes = seq.findPosition(sg.getStartRes());\r
 639 \r
 640         //FIND END RES\r
 641         //Need to find the residue preceeding index if gap\r
 642         endRes = 0;\r
 643 \r
 644         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 645         {\r
 646           ch = seq.getCharAt(j);\r
 647           if (!jalview.util.Comparison.isGap( (ch)))\r
 648           {\r
 649             endRes++;\r
 650           }\r
 651         }\r
 652 \r
 653         if(endRes>0)\r
 654         {\r
 655           endRes += seq.getStart() -1;\r
 656         }\r
 657 \r
 658         copiedSequences.append(seq.getName() + "\t" +\r
 659             startRes + "\t" +\r
 660             endRes + "\t" +\r
 661             seq.getSequence(sg.getStartRes(),\r
 662                 sg.getEndRes() + 1) + "\n");\r
 663     }\r
 664 \r
 665   }\r
 666 \r
 667   protected void pasteNew_actionPerformed()\r
 668   {\r
 669     paste(true);\r
 670   }\r
 671 \r
 672   protected void pasteThis_actionPerformed()\r
 673   {\r
 674     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 675                                    HistoryItem.PASTE));\r
 676     paste(false);\r
 677   }\r
 678 \r
 679   void paste(boolean newAlignment)\r
 680   {\r
 681     try\r
 682     {\r
 683       if (copiedSequences == null)\r
 684       {\r
 685         return;\r
 686       }\r
 687 \r
 688       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 689       Vector seqs = new Vector();\r
 690       while (st.hasMoreElements())\r
 691       {\r
 692         String name = st.nextToken();\r
 693         int start = Integer.parseInt(st.nextToken());\r
 694         int end = Integer.parseInt(st.nextToken());\r
 695         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 696 \r
 697         if (!newAlignment)\r
 698         {\r
 699           viewport.alignment.addSequence(sequence);\r
 700         }\r
 701         else\r
 702         {\r
 703           seqs.addElement(sequence);\r
 704         }\r
 705       }\r
 706 \r
 707       if (newAlignment)\r
 708       {\r
 709         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 710         for (int i = 0; i < seqs.size(); i++)\r
 711         {\r
 712           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 713         }\r
 714 \r
 715         String newtitle = new String("Copied sequences");\r
 716         if (getTitle().startsWith("Copied sequences"))\r
 717         {\r
 718           newtitle = getTitle();\r
 719         }\r
 720         else\r
 721         {\r
 722           newtitle = newtitle.concat("- from " + getTitle());\r
 723         }\r
 724         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 725 \r
 726         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 727                                          NEW_WINDOW_HEIGHT);\r
 728       }\r
 729       else\r
 730       {\r
 731         viewport.setEndSeq(viewport.alignment.getHeight());\r
 732         viewport.alignment.getWidth();\r
 733         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 734       }\r
 735 \r
 736     }\r
 737     catch (Exception ex)\r
 738     {} // could be anything being pasted in here\r
 739 \r
 740   }\r
 741 \r
 742   protected void cut_actionPerformed()\r
 743   {\r
 744     copy_actionPerformed();\r
 745     delete_actionPerformed();\r
 746   }\r
 747 \r
 748   protected void delete_actionPerformed()\r
 749   {\r
 750     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 751                                    HistoryItem.HIDE));\r
 752     if (viewport.getSelectionGroup() == null)\r
 753     {\r
 754       return;\r
 755     }\r
 756 \r
 757 \r
 758     SequenceGroup sg = viewport.getSelectionGroup();\r
 759     boolean allSequences = false;\r
 760     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 761           allSequences = true;\r
 762 \r
 763     for (int i = 0; i < sg.sequences.size(); i++)\r
 764     {\r
 765       SequenceI seq = sg.getSequenceAt(i);\r
 766       int index = viewport.getAlignment().findIndex(seq);\r
 767       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 768 \r
 769       // If the cut affects all sequences, remove highlighted columns\r
 770       if (allSequences)\r
 771       {\r
 772         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 773                                                      sg.getEndRes() + 1);\r
 774       }\r
 775 \r
 776 \r
 777       if (seq.getSequence().length() < 1)\r
 778       {\r
 779         viewport.getAlignment().deleteSequence(seq);\r
 780       }\r
 781       else\r
 782       {\r
 783         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 784       }\r
 785     }\r
 786 \r
 787     viewport.setSelectionGroup(null);\r
 788     viewport.alignment.deleteGroup(sg);\r
 789     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 790     if (viewport.getAlignment().getHeight() < 1)\r
 791     {\r
 792       try\r
 793       {\r
 794         this.setVisible(false);\r
 795       }\r
 796       catch (Exception ex)\r
 797       {}\r
 798     }\r
 799     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 800 \r
 801   }\r
 802 \r
 803   protected void deleteGroups_actionPerformed()\r
 804   {\r
 805     viewport.alignment.deleteAllGroups();\r
 806     viewport.setSelectionGroup(null);\r
 807 \r
 808     alignPanel.repaint();\r
 809   }\r
 810 \r
 811   public void selectAllSequenceMenuItem_actionPerformed()\r
 812   {\r
 813     SequenceGroup sg = new SequenceGroup();\r
 814     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 815     {\r
 816       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 817     }\r
 818     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 819     viewport.setSelectionGroup(sg);\r
 820     alignPanel.repaint();\r
 821     PaintRefresher.Refresh(null, viewport.alignment);\r
 822   }\r
 823 \r
 824   public void deselectAllSequenceMenuItem_actionPerformed()\r
 825   {\r
 826     viewport.setSelectionGroup(null);\r
 827     viewport.getColumnSelection().clear();\r
 828     viewport.setSelectionGroup(null);\r
 829     alignPanel.idPanel.idCanvas.searchResults = null;\r
 830     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
 831     alignPanel.repaint();\r
 832     PaintRefresher.Refresh(null, viewport.alignment);\r
 833   }\r
 834 \r
 835   public void invertSequenceMenuItem_actionPerformed()\r
 836   {\r
 837     SequenceGroup sg = viewport.getSelectionGroup();\r
 838     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 839     {\r
 840       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 841     }\r
 842 \r
 843     PaintRefresher.Refresh(null, viewport.alignment);\r
 844   }\r
 845 \r
 846   public void remove2LeftMenuItem_actionPerformed()\r
 847   {\r
 848     ColumnSelection colSel = viewport.getColumnSelection();\r
 849     if (colSel.size() > 0)\r
 850     {\r
 851       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 852                                      HistoryItem.HIDE));\r
 853       int min = colSel.getMin();\r
 854       viewport.getAlignment().trimLeft(min);\r
 855       colSel.compensateForEdit(0, min);\r
 856 \r
 857       if (viewport.getSelectionGroup() != null)\r
 858       {\r
 859         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 860       }\r
 861 \r
 862       Vector groups = viewport.alignment.getGroups();\r
 863       for (int i = 0; i < groups.size(); i++)\r
 864       {\r
 865         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 866         if (!sg.adjustForRemoveLeft(min))\r
 867         {\r
 868           viewport.alignment.deleteGroup(sg);\r
 869         }\r
 870       }\r
 871       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 872     }\r
 873   }\r
 874 \r
 875   public void remove2RightMenuItem_actionPerformed()\r
 876   {\r
 877     ColumnSelection colSel = viewport.getColumnSelection();\r
 878     if (colSel.size() > 0)\r
 879     {\r
 880       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 881                                      HistoryItem.HIDE));\r
 882       int max = colSel.getMax();\r
 883       viewport.getAlignment().trimRight(max);\r
 884       if (viewport.getSelectionGroup() != null)\r
 885       {\r
 886         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 887       }\r
 888 \r
 889       Vector groups = viewport.alignment.getGroups();\r
 890       for (int i = 0; i < groups.size(); i++)\r
 891       {\r
 892         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 893         if (!sg.adjustForRemoveRight(max))\r
 894         {\r
 895           viewport.alignment.deleteGroup(sg);\r
 896         }\r
 897       }\r
 898       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 899     }\r
 900 \r
 901   }\r
 902 \r
 903   public void removeGappedColumnMenuItem_actionPerformed()\r
 904   {\r
 905     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 906                                    viewport.alignment,\r
 907                                    HistoryItem.HIDE));\r
 908 \r
 909     //This is to maintain viewport position on first residue\r
 910     //of first sequence\r
 911     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 912     int startRes = seq.findPosition(viewport.startRes);\r
 913 \r
 914     viewport.getAlignment().removeGaps();\r
 915 \r
 916     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 917 \r
 918     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 919   }\r
 920 \r
 921   public void removeAllGapsMenuItem_actionPerformed()\r
 922   {\r
 923     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 924                                    HistoryItem.HIDE));\r
 925 \r
 926     //This is to maintain viewport position on first residue\r
 927     //of first sequence\r
 928     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 929     int startRes = seq.findPosition(viewport.startRes);\r
 930 \r
 931     SequenceI current;\r
 932     int jSize;\r
 933 \r
 934     Vector seqs=null;\r
 935 \r
 936     int start=0, end = viewport.alignment.getWidth();\r
 937 \r
 938     if (viewport.getSelectionGroup() != null\r
 939         && viewport.getSelectionGroup().sequences != null\r
 940         && viewport.getSelectionGroup().sequences.size()>0)\r
 941     {\r
 942       seqs = viewport.getSelectionGroup().sequences;\r
 943       start = viewport.getSelectionGroup().getStartRes();\r
 944       end = viewport.getSelectionGroup().getEndRes()+1;\r
 945     }\r
 946     else\r
 947       seqs = viewport.alignment.getSequences();\r
 948 \r
 949     for (int i = 0; i < seqs.size(); i++)\r
 950     {\r
 951       current = (SequenceI) seqs.elementAt(i);\r
 952       jSize = current.getLength();\r
 953 \r
 954       // Removing a range is much quicker than removing gaps\r
 955       // one by one for long sequences\r
 956       int j = start;\r
 957       int rangeStart=-1, rangeEnd=-1;\r
 958 \r
 959       do\r
 960       {\r
 961         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 962         {\r
 963           if(rangeStart==-1)\r
 964            {\r
 965              rangeStart = j;\r
 966              rangeEnd = j+1;\r
 967            }\r
 968            else\r
 969            {\r
 970              rangeEnd++;\r
 971            }\r
 972            j++;\r
 973         }\r
 974         else\r
 975         {\r
 976           if(rangeStart>-1)\r
 977           {\r
 978             current.deleteChars(rangeStart, rangeEnd);\r
 979             j-=rangeEnd-rangeStart;\r
 980             jSize-=rangeEnd-rangeStart;\r
 981             rangeStart = -1;\r
 982             rangeEnd = -1;\r
 983           }\r
 984           else\r
 985             j++;\r
 986         }\r
 987       }\r
 988       while (j < end && j < jSize);\r
 989       if(rangeStart>-1)\r
 990       {\r
 991        current.deleteChars(rangeStart, rangeEnd);\r
 992       }\r
 993     }\r
 994     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 995     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 996   }\r
 997 \r
 998   public void alignmentChanged()\r
 999   {\r
1000     viewport.updateConsensus();\r
1001     viewport.updateConservation ();\r
1002     resetAllColourSchemes();\r
1003     if(alignPanel.overviewPanel!=null)\r
1004       alignPanel.overviewPanel.updateOverviewImage();\r
1005 \r
1006     viewport.alignment.adjustSequenceAnnotations();\r
1007     alignPanel.repaint();\r
1008   }\r
1009 \r
1010   void resetAllColourSchemes()\r
1011   {\r
1012     ColourSchemeI cs = viewport.globalColourScheme;\r
1013     if(cs!=null)\r
1014     {\r
1015       if (cs instanceof ClustalxColourScheme)\r
1016       {\r
1017         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1018             resetClustalX(viewport.alignment.getSequences(),\r
1019                           viewport.alignment.getWidth());\r
1020       }\r
1021 \r
1022       cs.setConsensus(viewport.vconsensus);\r
1023       if (cs.conservationApplied())\r
1024       {\r
1025         Alignment al = (Alignment) viewport.alignment;\r
1026         Conservation c = new Conservation("All",\r
1027                                           ResidueProperties.propHash, 3,\r
1028                                           al.getSequences(), 0,\r
1029                                           al.getWidth() - 1);\r
1030         c.calculate();\r
1031         c.verdict(false, viewport.ConsPercGaps);\r
1032 \r
1033         cs.setConservation(c);\r
1034       }\r
1035     }\r
1036 \r
1037     int s, sSize = viewport.alignment.getGroups().size();\r
1038     for(s=0; s<sSize; s++)\r
1039     {\r
1040       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1041       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1042       {\r
1043         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
1044       }\r
1045       sg.recalcConservation();\r
1046     }\r
1047   }\r
1048 \r
1049 \r
1050 \r
1051   public void findMenuItem_actionPerformed()\r
1052   {\r
1053     new Finder(alignPanel);\r
1054   }\r
1055 \r
1056   public void font_actionPerformed()\r
1057   {\r
1058     new FontChooser(alignPanel);\r
1059   }\r
1060 \r
1061 \r
1062   public void seqLimits_itemStateChanged()\r
1063   {\r
1064     viewport.setShowJVSuffix(seqLimits.getState());\r
1065     alignPanel.fontChanged();\r
1066     alignPanel.repaint();\r
1067   }\r
1068 \r
1069 \r
1070   protected void colourTextMenuItem_actionPerformed()\r
1071   {\r
1072     viewport.setColourText(colourTextMenuItem.getState());\r
1073     alignPanel.repaint();\r
1074   }\r
1075 \r
1076   protected void wrapMenuItem_actionPerformed()\r
1077   {\r
1078     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1079     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1080     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1081     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1082     scaleRight.setEnabled(wrapMenuItem.getState());\r
1083     alignPanel.repaint();\r
1084   }\r
1085 \r
1086   protected void scaleAbove_actionPerformed()\r
1087   {\r
1088     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1089     alignPanel.repaint();\r
1090   }\r
1091 \r
1092   protected void scaleLeft_actionPerformed()\r
1093   {\r
1094     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1095     alignPanel.repaint();\r
1096   }\r
1097 \r
1098   protected void scaleRight_actionPerformed()\r
1099   {\r
1100     viewport.setScaleRightWrapped(scaleRight.getState());\r
1101     alignPanel.repaint();\r
1102   }\r
1103 \r
1104   public void viewBoxesMenuItem_actionPerformed()\r
1105   {\r
1106     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1107     alignPanel.repaint();\r
1108   }\r
1109 \r
1110   public void viewTextMenuItem_actionPerformed()\r
1111   {\r
1112     viewport.setShowText(viewTextMenuItem.getState());\r
1113     alignPanel.repaint();\r
1114   }\r
1115 \r
1116   protected void renderGapsMenuItem_actionPerformed()\r
1117   {\r
1118     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1119     alignPanel.repaint();\r
1120   }\r
1121 \r
1122   public void annotationPanelMenuItem_actionPerformed()\r
1123   {\r
1124     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1125     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1126   }\r
1127 \r
1128   public void featureSettings_actionPerformed()\r
1129   {\r
1130     new FeatureSettings(viewport, alignPanel);\r
1131   }\r
1132 \r
1133   public void overviewMenuItem_actionPerformed()\r
1134   {\r
1135     if (alignPanel.overviewPanel != null)\r
1136     {\r
1137       return;\r
1138     }\r
1139 \r
1140     Frame frame = new Frame();\r
1141     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1142     frame.add(overview);\r
1143     // +50 must allow for applet frame window\r
1144     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1145                                      overview.preferredSize().width,\r
1146                                      overview.preferredSize().height + 50);\r
1147 \r
1148     frame.pack();\r
1149     frame.addWindowListener(new WindowAdapter()\r
1150     {\r
1151       public void windowClosing(WindowEvent e)\r
1152       {\r
1153         alignPanel.setOverviewPanel(null);\r
1154       };\r
1155     });\r
1156 \r
1157     alignPanel.setOverviewPanel(overview);\r
1158 \r
1159   }\r
1160 \r
1161   protected void noColourmenuItem_actionPerformed()\r
1162   {\r
1163     changeColour(null);\r
1164   }\r
1165 \r
1166   public void clustalColour_actionPerformed()\r
1167   {\r
1168     abovePIDThreshold.setState(false);\r
1169     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1170                                           viewport.alignment.getWidth()));\r
1171   }\r
1172 \r
1173   public void zappoColour_actionPerformed()\r
1174   {\r
1175     changeColour(new ZappoColourScheme());\r
1176   }\r
1177 \r
1178   public void taylorColour_actionPerformed()\r
1179   {\r
1180     changeColour(new TaylorColourScheme());\r
1181   }\r
1182 \r
1183   public void hydrophobicityColour_actionPerformed()\r
1184   {\r
1185     changeColour(new HydrophobicColourScheme());\r
1186   }\r
1187 \r
1188   public void helixColour_actionPerformed()\r
1189   {\r
1190     changeColour(new HelixColourScheme());\r
1191   }\r
1192 \r
1193   public void strandColour_actionPerformed()\r
1194   {\r
1195     changeColour(new StrandColourScheme());\r
1196   }\r
1197 \r
1198   public void turnColour_actionPerformed()\r
1199   {\r
1200     changeColour(new TurnColourScheme());\r
1201   }\r
1202 \r
1203   public void buriedColour_actionPerformed()\r
1204   {\r
1205     changeColour(new BuriedColourScheme());\r
1206   }\r
1207 \r
1208   public void nucleotideColour_actionPerformed()\r
1209   {\r
1210     changeColour(new NucleotideColourScheme());\r
1211   }\r
1212 \r
1213   protected void applyToAllGroups_actionPerformed()\r
1214   {\r
1215     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1216   }\r
1217 \r
1218   void changeColour(ColourSchemeI cs)\r
1219   {\r
1220     int threshold = 0;\r
1221 \r
1222     if(cs!=null)\r
1223     {\r
1224       if (viewport.getAbovePIDThreshold())\r
1225       {\r
1226         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1227 \r
1228         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1229 \r
1230         viewport.setGlobalColourScheme(cs);\r
1231       }\r
1232       else\r
1233       {\r
1234         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1235       }\r
1236 \r
1237       if (viewport.getConservationSelected())\r
1238       {\r
1239 \r
1240         Alignment al = (Alignment) viewport.alignment;\r
1241         Conservation c = new Conservation("All",\r
1242                                           ResidueProperties.propHash, 3,\r
1243                                           al.getSequences(), 0,\r
1244                                           al.getWidth() - 1);\r
1245 \r
1246         c.calculate();\r
1247         c.verdict(false, viewport.ConsPercGaps);\r
1248 \r
1249         cs.setConservation(c);\r
1250 \r
1251         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1252             "Background"));\r
1253 \r
1254       }\r
1255       else\r
1256       {\r
1257         cs.setConservation(null);\r
1258       }\r
1259 \r
1260       cs.setConsensus(viewport.vconsensus);\r
1261 \r
1262     }\r
1263     viewport.setGlobalColourScheme(cs);\r
1264 \r
1265     if (viewport.getColourAppliesToAllGroups())\r
1266     {\r
1267       Vector groups = viewport.alignment.getGroups();\r
1268       for (int i = 0; i < groups.size(); i++)\r
1269       {\r
1270         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1271 \r
1272         if(cs==null)\r
1273         {\r
1274           sg.cs = null;\r
1275           continue;\r
1276         }\r
1277         if (cs instanceof ClustalxColourScheme)\r
1278         {\r
1279           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1280         }\r
1281         else\r
1282         {\r
1283           try\r
1284           {\r
1285             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1286           }\r
1287           catch (Exception ex)\r
1288           {\r
1289             ex.printStackTrace();\r
1290             sg.cs = cs;\r
1291           }\r
1292         }\r
1293 \r
1294         if (viewport.getAbovePIDThreshold()\r
1295             || cs instanceof PIDColourScheme\r
1296             || cs instanceof Blosum62ColourScheme)\r
1297         {\r
1298           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1299           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1300         }\r
1301         else\r
1302           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1303 \r
1304         if (viewport.getConservationSelected())\r
1305         {\r
1306           Conservation c = new Conservation("Group",\r
1307                                             ResidueProperties.propHash, 3,\r
1308                                             sg.sequences, 0,\r
1309                                             viewport.alignment.getWidth() - 1);\r
1310           c.calculate();\r
1311           c.verdict(false, viewport.ConsPercGaps);\r
1312           sg.cs.setConservation(c);\r
1313         }\r
1314         else\r
1315         {\r
1316           sg.cs.setConservation(null);\r
1317           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1318         }\r
1319 \r
1320       }\r
1321     }\r
1322 \r
1323 \r
1324     if (alignPanel.getOverviewPanel() != null)\r
1325     {\r
1326       alignPanel.getOverviewPanel().updateOverviewImage();\r
1327     }\r
1328 \r
1329     alignPanel.repaint();\r
1330   }\r
1331 \r
1332 \r
1333 \r
1334   protected void modifyPID_actionPerformed()\r
1335   {\r
1336     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1337     {\r
1338       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1339                                      "Background");\r
1340       SliderPanel.showPIDSlider();\r
1341     }\r
1342   }\r
1343 \r
1344   protected void modifyConservation_actionPerformed()\r
1345   {\r
1346     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1347     {\r
1348       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1349                                         "Background");\r
1350       SliderPanel.showConservationSlider();\r
1351     }\r
1352   }\r
1353 \r
1354   protected void conservationMenuItem_actionPerformed()\r
1355   {\r
1356     viewport.setConservationSelected(conservationMenuItem.getState());\r
1357 \r
1358     viewport.setAbovePIDThreshold(false);\r
1359     abovePIDThreshold.setState(false);\r
1360 \r
1361     changeColour(viewport.getGlobalColourScheme());\r
1362 \r
1363     modifyConservation_actionPerformed();\r
1364   }\r
1365 \r
1366   public void abovePIDThreshold_actionPerformed()\r
1367   {\r
1368     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1369 \r
1370     conservationMenuItem.setState(false);\r
1371     viewport.setConservationSelected(false);\r
1372 \r
1373     changeColour(viewport.getGlobalColourScheme());\r
1374 \r
1375     modifyPID_actionPerformed();\r
1376   }\r
1377 \r
1378   public void userDefinedColour_actionPerformed()\r
1379   {\r
1380     new UserDefinedColours(alignPanel, null);\r
1381   }\r
1382 \r
1383   public void PIDColour_actionPerformed()\r
1384   {\r
1385     changeColour(new PIDColourScheme());\r
1386   }\r
1387 \r
1388   public void BLOSUM62Colour_actionPerformed()\r
1389   {\r
1390     changeColour(new Blosum62ColourScheme());\r
1391   }\r
1392 \r
1393   public void sortPairwiseMenuItem_actionPerformed()\r
1394   {\r
1395     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1396                                    HistoryItem.SORT));\r
1397     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1398                               viewport.getAlignment().getSequenceAt(0));\r
1399     alignPanel.repaint();\r
1400   }\r
1401 \r
1402   public void sortIDMenuItem_actionPerformed()\r
1403   {\r
1404     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1405                                    HistoryItem.SORT));\r
1406     AlignmentSorter.sortByID(viewport.getAlignment());\r
1407     alignPanel.repaint();\r
1408   }\r
1409 \r
1410   public void sortGroupMenuItem_actionPerformed()\r
1411   {\r
1412     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1413                                    HistoryItem.SORT));\r
1414     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1415     alignPanel.repaint();\r
1416 \r
1417   }\r
1418 \r
1419   public void removeRedundancyMenuItem_actionPerformed()\r
1420   {\r
1421     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1422     Frame frame = new Frame();\r
1423     frame.add(sp);\r
1424     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1425                                      400, 120);\r
1426 \r
1427   }\r
1428 \r
1429   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1430   {\r
1431     if (viewport.getSelectionGroup().getSize() > 1)\r
1432     {\r
1433       Frame frame = new Frame();\r
1434       frame.add(new PairwiseAlignPanel(alignPanel));\r
1435       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1436     }\r
1437   }\r
1438 \r
1439   public void PCAMenuItem_actionPerformed()\r
1440   {\r
1441     //are the sequences aligned?\r
1442     if (!viewport.alignment.isAligned())\r
1443     {\r
1444       SequenceI current;\r
1445       int Width = viewport.getAlignment().getWidth();\r
1446 \r
1447       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1448            i++)\r
1449       {\r
1450         current = viewport.getAlignment().getSequenceAt(i);\r
1451 \r
1452         if (current.getLength() < Width)\r
1453         {\r
1454           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1455         }\r
1456       }\r
1457       alignPanel.repaint();\r
1458     }\r
1459 \r
1460     if ( (viewport.getSelectionGroup() != null &&\r
1461           viewport.getSelectionGroup().getSize() < 4 &&\r
1462           viewport.getSelectionGroup().getSize() > 0)\r
1463         || viewport.getAlignment().getHeight() < 4)\r
1464     {\r
1465       return;\r
1466     }\r
1467 \r
1468     try\r
1469     {\r
1470       new PCAPanel(viewport);\r
1471     }\r
1472     catch (java.lang.OutOfMemoryError ex)\r
1473     {\r
1474     }\r
1475 \r
1476   }\r
1477 \r
1478   public void averageDistanceTreeMenuItem_actionPerformed()\r
1479   {\r
1480     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1481   }\r
1482 \r
1483   public void neighbourTreeMenuItem_actionPerformed()\r
1484   {\r
1485     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1486   }\r
1487 \r
1488   protected void njTreeBlosumMenuItem_actionPerformed()\r
1489   {\r
1490     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1491   }\r
1492 \r
1493   protected void avTreeBlosumMenuItem_actionPerformed()\r
1494   {\r
1495     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1496   }\r
1497 \r
1498   void NewTreePanel(String type, String pwType, String title)\r
1499   {\r
1500     //are the sequences aligned?\r
1501     if (!viewport.alignment.isAligned())\r
1502     {\r
1503       SequenceI current;\r
1504       int Width = viewport.getAlignment().getWidth();\r
1505 \r
1506       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1507            i++)\r
1508       {\r
1509         current = viewport.getAlignment().getSequenceAt(i);\r
1510 \r
1511         if (current.getLength() < Width)\r
1512         {\r
1513           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1514         }\r
1515       }\r
1516       alignPanel.repaint();\r
1517 \r
1518     }\r
1519 \r
1520     final TreePanel tp;\r
1521     if (viewport.getSelectionGroup() != null &&\r
1522         viewport.getSelectionGroup().getSize() > 3)\r
1523     {\r
1524       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1525                          pwType,\r
1526                          0, viewport.alignment.getWidth());\r
1527     }\r
1528     else\r
1529     {\r
1530       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1531                          type, pwType, 0, viewport.alignment.getWidth());\r
1532     }\r
1533 \r
1534     addTreeMenuItem(tp, title);\r
1535 \r
1536     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1537   }\r
1538 \r
1539   public void addTreeMenuItem(final TreePanel treePanel, String title)\r
1540   {\r
1541     final MenuItem item = new MenuItem(title);\r
1542     sortByTreeMenu.add(item);\r
1543     item.addActionListener(new java.awt.event.ActionListener()\r
1544     {\r
1545       public void actionPerformed(ActionEvent evt)\r
1546       {\r
1547         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1548                                        HistoryItem.SORT));\r
1549         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1550         alignPanel.repaint();\r
1551       }\r
1552     });\r
1553 \r
1554     treePanel.addWindowListener(new WindowAdapter()\r
1555     {\r
1556       public void windowClosing(WindowEvent e)\r
1557       {\r
1558         sortByTreeMenu.remove(item);\r
1559       };\r
1560     });\r
1561   }\r
1562 \r
1563   protected void documentation_actionPerformed()\r
1564   {\r
1565     showURL("http://www.jalview.org/help.html", "HELP");\r
1566   }\r
1567 \r
1568   protected void about_actionPerformed()\r
1569   {\r
1570 \r
1571     class AboutPanel extends Canvas\r
1572     {\r
1573       String version;\r
1574       public AboutPanel(String version)\r
1575       { this.version = version; }\r
1576 \r
1577       public void paint(Graphics g)\r
1578       {\r
1579         g.setColor(Color.white);\r
1580         g.fillRect(0, 0, getSize().width, getSize().height);\r
1581         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1582         FontMetrics fm = g.getFontMetrics();\r
1583         int fh = fm.getHeight();\r
1584         int y = 5, x = 7;\r
1585         g.setColor(Color.black);\r
1586         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1587         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1588         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1589         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1590                      x, y += fh * 2);\r
1591         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1592                      x, y += fh);\r
1593         g.drawString(\r
1594             "For any issues relating to Jalview, email help@jalview.org", x,\r
1595             y += fh);\r
1596         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1597         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1598                      x, y += fh);\r
1599         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1600       }\r
1601     }\r
1602 \r
1603     String version = "test";\r
1604     java.net.URL url = getClass().getResource("/.build_properties");\r
1605     if (url != null)\r
1606     {\r
1607       try\r
1608       {\r
1609         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1610             url.openStream()));\r
1611         String line;\r
1612         while ( (line = reader.readLine()) != null)\r
1613         {\r
1614           if (line.indexOf("VERSION") > -1)\r
1615           {\r
1616             version = line.substring(line.indexOf("=") + 1);\r
1617           }\r
1618         }\r
1619       }\r
1620       catch (Exception ex)\r
1621       {\r
1622         ex.printStackTrace();\r
1623       }\r
1624     }\r
1625 \r
1626 \r
1627     Frame frame = new Frame();\r
1628     frame.add(new AboutPanel(version));\r
1629     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1630 \r
1631   }\r
1632 \r
1633   public void showURL(String url, String target)\r
1634   {\r
1635     if (applet == null)\r
1636     {\r
1637       System.out.println("Not running as applet - no browser available.");\r
1638     }\r
1639     else\r
1640     {\r
1641       try\r
1642       {\r
1643         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1644                                                target);\r
1645       }\r
1646       catch (Exception ex)\r
1647       {\r
1648         ex.printStackTrace();\r
1649       }\r
1650     }\r
1651   }\r
1652 \r
1653 \r
1654   //////////////////////////////////////////////////////////////////////////////////\r
1655   //JBuilder Graphics here\r
1656 \r
1657     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1658     protected Menu fileMenu = new Menu();\r
1659     protected MenuItem closeMenuItem = new MenuItem();\r
1660     protected Menu editMenu = new Menu();\r
1661     protected Menu viewMenu = new Menu();\r
1662     protected Menu colourMenu = new Menu();\r
1663     protected Menu calculateMenu = new Menu();\r
1664     protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
1665     protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
1666     protected MenuItem invertSequenceMenuItem = new MenuItem();\r
1667     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1668     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1669     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1670     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1671     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1672     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1673     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1674     protected MenuItem sortIDMenuItem = new MenuItem();\r
1675     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1676     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1677     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1678     protected MenuItem PCAMenuItem = new MenuItem();\r
1679     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1680     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1681     BorderLayout borderLayout1 = new BorderLayout();\r
1682     public Label statusBar = new Label();\r
1683     protected Menu outputTextboxMenu = new Menu();\r
1684     protected MenuItem clustalColour = new MenuItem();\r
1685     protected MenuItem zappoColour = new MenuItem();\r
1686     protected MenuItem taylorColour = new MenuItem();\r
1687     protected MenuItem hydrophobicityColour = new MenuItem();\r
1688     protected MenuItem helixColour = new MenuItem();\r
1689     protected MenuItem strandColour = new MenuItem();\r
1690     protected MenuItem turnColour = new MenuItem();\r
1691     protected MenuItem buriedColour = new MenuItem();\r
1692     protected MenuItem userDefinedColour = new MenuItem();\r
1693     protected MenuItem PIDColour = new MenuItem();\r
1694     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1695     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1696     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1697     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1698     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1699     MenuItem overviewMenuItem = new MenuItem();\r
1700     protected MenuItem undoMenuItem = new MenuItem();\r
1701     protected MenuItem redoMenuItem = new MenuItem();\r
1702     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1703     MenuItem noColourmenuItem = new MenuItem();\r
1704     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1705     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1706     MenuItem findMenuItem = new MenuItem();\r
1707     Menu searchMenu = new Menu();\r
1708     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1709     protected MenuItem nucleotideColour = new MenuItem();\r
1710     MenuItem deleteGroups = new MenuItem();\r
1711     MenuItem delete = new MenuItem();\r
1712     MenuItem copy = new MenuItem();\r
1713     MenuItem cut = new MenuItem();\r
1714     Menu pasteMenu = new Menu();\r
1715     MenuItem pasteNew = new MenuItem();\r
1716     MenuItem pasteThis = new MenuItem();\r
1717     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1718     protected MenuItem font = new MenuItem();\r
1719     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1720     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1721     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1722     MenuItem modifyPID = new MenuItem();\r
1723     MenuItem modifyConservation = new MenuItem();\r
1724     protected Menu sortByTreeMenu = new Menu();\r
1725     Menu sort = new Menu();\r
1726     Menu calculate = new Menu();\r
1727     MenuItem inputText = new MenuItem();\r
1728     Menu helpMenu = new Menu();\r
1729     MenuItem documentation = new MenuItem();\r
1730     MenuItem about = new MenuItem();\r
1731     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1732   Panel embeddedMenu;\r
1733   Label embeddedEdit;\r
1734   Label embeddedSearch;\r
1735   Label embeddedView;\r
1736   Label embeddedColour;\r
1737   Label embeddedFile;\r
1738   Label embeddedHelp;\r
1739   Label embeddedCalculate;\r
1740   FlowLayout flowLayout1;\r
1741 \r
1742   private void jbInit() throws Exception {\r
1743 \r
1744       setMenuBar(alignFrameMenuBar);\r
1745 \r
1746       MenuItem item;\r
1747 \r
1748       // dynamically fill save as menu with available formats\r
1749       for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
1750       {\r
1751 \r
1752         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
1753                             elementAt(\r
1754                                 i));\r
1755         item.addActionListener(new java.awt.event.ActionListener()\r
1756         {\r
1757           public void actionPerformed(ActionEvent e)\r
1758           {\r
1759             outputText_actionPerformed(e);\r
1760           }\r
1761         });\r
1762 \r
1763         outputTextboxMenu.add(item);\r
1764       }\r
1765 \r
1766         fileMenu.setLabel("File");\r
1767         closeMenuItem.setLabel("Close");\r
1768         closeMenuItem.addActionListener(this);\r
1769         editMenu.setLabel("Edit");\r
1770         viewMenu.setLabel("View");\r
1771         colourMenu.setLabel("Colour");\r
1772         calculateMenu.setLabel("Calculate");\r
1773         selectAllSequenceMenuItem.setLabel("Select all");\r
1774         selectAllSequenceMenuItem.addActionListener(this);\r
1775         deselectAllSequenceMenuItem.setLabel("Deselect All");\r
1776         deselectAllSequenceMenuItem.addActionListener(this);\r
1777         invertSequenceMenuItem.setLabel("Invert Selection");\r
1778         invertSequenceMenuItem.addActionListener(this);\r
1779         remove2LeftMenuItem.setLabel("Remove Left");\r
1780         remove2LeftMenuItem.addActionListener(this);\r
1781         remove2RightMenuItem.setLabel("Remove Right");\r
1782         remove2RightMenuItem.addActionListener(this);\r
1783         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1784         removeGappedColumnMenuItem.addActionListener(this);\r
1785         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1786         removeAllGapsMenuItem.addActionListener(this);\r
1787         viewBoxesMenuItem.setLabel("Boxes");\r
1788         viewBoxesMenuItem.setState(true);\r
1789         viewBoxesMenuItem.addItemListener(this);\r
1790         viewTextMenuItem.setLabel("Text");\r
1791         viewTextMenuItem.setState(true);\r
1792         viewTextMenuItem.addItemListener(this);\r
1793         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1794         sortPairwiseMenuItem.addActionListener(this);\r
1795         sortIDMenuItem.setLabel("by ID");\r
1796         sortIDMenuItem.addActionListener(this);\r
1797         sortGroupMenuItem.setLabel("by Group");\r
1798         sortGroupMenuItem.addActionListener(this);\r
1799         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1800         removeRedundancyMenuItem.addActionListener(this);\r
1801         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1802         pairwiseAlignmentMenuItem.addActionListener(this);\r
1803         PCAMenuItem.setLabel("Principal Component Analysis");\r
1804         PCAMenuItem.addActionListener(this);\r
1805         averageDistanceTreeMenuItem.setLabel(\r
1806             "Average Distance Using % Identity");\r
1807         averageDistanceTreeMenuItem.addActionListener(this);\r
1808         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1809         neighbourTreeMenuItem.addActionListener(this);\r
1810         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1811         statusBar.setBackground(Color.white);\r
1812         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1813         statusBar.setText("Status bar");\r
1814         outputTextboxMenu.setLabel("Output to Textbox");\r
1815         clustalColour.setLabel("Clustalx");\r
1816 \r
1817         clustalColour.addActionListener(this);\r
1818         zappoColour.setLabel("Zappo");\r
1819         zappoColour.addActionListener(this);\r
1820         taylorColour.setLabel("Taylor");\r
1821         taylorColour.addActionListener(this);\r
1822         hydrophobicityColour.setLabel("Hydrophobicity");\r
1823         hydrophobicityColour.addActionListener(this);\r
1824         helixColour.setLabel("Helix Propensity");\r
1825         helixColour.addActionListener(this);\r
1826         strandColour.setLabel("Strand Propensity");\r
1827         strandColour.addActionListener(this);\r
1828         turnColour.setLabel("Turn Propensity");\r
1829         turnColour.addActionListener(this);\r
1830         buriedColour.setLabel("Buried Index");\r
1831         buriedColour.addActionListener(this);\r
1832         userDefinedColour.setLabel("User Defined...");\r
1833         userDefinedColour.addActionListener(this);\r
1834         PIDColour.setLabel("Percentage Identity");\r
1835         PIDColour.addActionListener(this);\r
1836         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
1837         BLOSUM62Colour.addActionListener(this);\r
1838         avDistanceTreeBlosumMenuItem.setLabel(\r
1839             "Average Distance Using BLOSUM62");\r
1840         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
1841         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
1842         njTreeBlosumMenuItem.addActionListener(this);\r
1843         annotationPanelMenuItem.setLabel("Show Annotations");\r
1844         annotationPanelMenuItem.addItemListener(this);\r
1845         colourTextMenuItem.setLabel("Colour Text");\r
1846         colourTextMenuItem.addItemListener(this);\r
1847         overviewMenuItem.setLabel("Overview Window");\r
1848         overviewMenuItem.addActionListener(this);\r
1849         undoMenuItem.setEnabled(false);\r
1850         undoMenuItem.setLabel("Undo");\r
1851         undoMenuItem.addActionListener(this);\r
1852         redoMenuItem.setEnabled(false);\r
1853         redoMenuItem.setLabel("Redo");\r
1854         redoMenuItem.addActionListener(this);\r
1855         conservationMenuItem.setLabel("by Conservation");\r
1856         conservationMenuItem.addItemListener(this);\r
1857         noColourmenuItem.setLabel("None");\r
1858         noColourmenuItem.addActionListener(this);\r
1859         wrapMenuItem.setLabel("Wrap");\r
1860         wrapMenuItem.addItemListener(this);\r
1861         renderGapsMenuItem.setLabel("Show Gaps");\r
1862         renderGapsMenuItem.setState(true);\r
1863         renderGapsMenuItem.addItemListener(this);\r
1864         findMenuItem.setLabel("Find...");\r
1865         findMenuItem.addActionListener(this);\r
1866         searchMenu.setLabel("Search");\r
1867 \r
1868         abovePIDThreshold.setLabel("Above Identity Threshold");\r
1869         abovePIDThreshold.addItemListener(this);\r
1870         nucleotideColour.setLabel("Nucleotide");\r
1871         nucleotideColour.addActionListener(this);\r
1872         deleteGroups.setLabel("Undefine Groups");\r
1873         deleteGroups.addActionListener(this);\r
1874         copy.setLabel("Copy");\r
1875         copy.addActionListener(this);\r
1876         cut.setLabel("Cut");\r
1877         cut.addActionListener(this);\r
1878         delete.setLabel("Delete");\r
1879         delete.addActionListener(this);\r
1880         pasteMenu.setLabel("Paste");\r
1881         pasteNew.setLabel("To New Alignment");\r
1882         pasteNew.addActionListener(this);\r
1883         pasteThis.setLabel("Add To This Alignment");\r
1884         pasteThis.addActionListener(this);\r
1885         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
1886         applyToAllGroups.setState(true);\r
1887         applyToAllGroups.addItemListener(this);\r
1888         font.setLabel("Font...");\r
1889         font.addActionListener(this);\r
1890         scaleAbove.setLabel("Scale Above");\r
1891         scaleAbove.setState(true);\r
1892         scaleAbove.setEnabled(false);\r
1893         scaleAbove.addItemListener(this);\r
1894         scaleLeft.setEnabled(false);\r
1895         scaleLeft.setState(true);\r
1896         scaleLeft.setLabel("Scale Left");\r
1897         scaleLeft.addItemListener(this);\r
1898         scaleRight.setEnabled(false);\r
1899         scaleRight.setState(true);\r
1900         scaleRight.setLabel("Scale Right");\r
1901         scaleRight.addItemListener(this);\r
1902         modifyPID.setLabel("Modify Identity Threshold...");\r
1903         modifyPID.addActionListener(this);\r
1904         modifyConservation.setLabel("Modify Conservation Threshold...");\r
1905         modifyConservation.addActionListener(this);\r
1906         sortByTreeMenu.setLabel("By Tree Order");\r
1907         sort.setLabel("Sort");\r
1908         calculate.setLabel("Calculate Tree");\r
1909         inputText.setLabel("Input from textbox");\r
1910         inputText.addActionListener(this);\r
1911 \r
1912         helpMenu.setLabel("Help");\r
1913         documentation.setLabel("Documentation");\r
1914         documentation.addActionListener(this);\r
1915 \r
1916         about.setLabel("About...");\r
1917         about.addActionListener(this);\r
1918           seqLimits.setState(true);\r
1919     seqLimits.setLabel("Show Sequence Limits");\r
1920     seqLimits.addItemListener(this);\r
1921     featureSettings.setLabel("Feature Settings...");\r
1922     featureSettings.addActionListener(this);\r
1923     sequenceFeatures.setLabel("Sequence Features");\r
1924     sequenceFeatures.addItemListener(this);\r
1925     sequenceFeatures.setState(true);\r
1926 \r
1927     alignFrameMenuBar.add(fileMenu);\r
1928         alignFrameMenuBar.add(editMenu);\r
1929         alignFrameMenuBar.add(searchMenu);\r
1930         alignFrameMenuBar.add(viewMenu);\r
1931         alignFrameMenuBar.add(colourMenu);\r
1932         alignFrameMenuBar.add(calculateMenu);\r
1933         alignFrameMenuBar.add(helpMenu);\r
1934         fileMenu.add(inputText);\r
1935         fileMenu.add(outputTextboxMenu);\r
1936         fileMenu.addSeparator();\r
1937         fileMenu.add(closeMenuItem);\r
1938         editMenu.add(undoMenuItem);\r
1939         editMenu.add(redoMenuItem);\r
1940         editMenu.add(cut);\r
1941         editMenu.add(copy);\r
1942         editMenu.add(pasteMenu);\r
1943         editMenu.add(delete);\r
1944         editMenu.addSeparator();\r
1945         editMenu.add(selectAllSequenceMenuItem);\r
1946         editMenu.add(deselectAllSequenceMenuItem);\r
1947         editMenu.add(invertSequenceMenuItem);\r
1948         editMenu.add(deleteGroups);\r
1949         editMenu.addSeparator();\r
1950         editMenu.add(remove2LeftMenuItem);\r
1951         editMenu.add(remove2RightMenuItem);\r
1952         editMenu.add(removeGappedColumnMenuItem);\r
1953         editMenu.add(removeAllGapsMenuItem);\r
1954         editMenu.add(removeRedundancyMenuItem);\r
1955         searchMenu.add(findMenuItem);\r
1956         viewMenu.add(font);\r
1957         viewMenu.addSeparator();\r
1958     viewMenu.add(seqLimits);\r
1959         viewMenu.addSeparator();\r
1960     viewMenu.add(wrapMenuItem);\r
1961         viewMenu.add(scaleAbove);\r
1962         viewMenu.add(scaleLeft);\r
1963         viewMenu.add(scaleRight);\r
1964         viewMenu.addSeparator();\r
1965     viewMenu.add(viewBoxesMenuItem);\r
1966         viewMenu.add(viewTextMenuItem);\r
1967         viewMenu.add(colourTextMenuItem);\r
1968         viewMenu.add(renderGapsMenuItem);\r
1969         viewMenu.add(annotationPanelMenuItem);\r
1970     viewMenu.addSeparator();\r
1971         viewMenu.add(overviewMenuItem);\r
1972         colourMenu.add(applyToAllGroups);\r
1973         colourMenu.addSeparator();\r
1974         colourMenu.add(noColourmenuItem);\r
1975         colourMenu.add(clustalColour);\r
1976         colourMenu.add(BLOSUM62Colour);\r
1977         colourMenu.add(PIDColour);\r
1978         colourMenu.add(zappoColour);\r
1979         colourMenu.add(taylorColour);\r
1980         colourMenu.add(hydrophobicityColour);\r
1981         colourMenu.add(helixColour);\r
1982         colourMenu.add(strandColour);\r
1983         colourMenu.add(turnColour);\r
1984         colourMenu.add(buriedColour);\r
1985         colourMenu.add(nucleotideColour);\r
1986         colourMenu.add(userDefinedColour);\r
1987         colourMenu.addSeparator();\r
1988         colourMenu.add(conservationMenuItem);\r
1989         colourMenu.add(modifyConservation);\r
1990         colourMenu.add(abovePIDThreshold);\r
1991         colourMenu.add(modifyPID);\r
1992         calculateMenu.add(sort);\r
1993         calculateMenu.add(calculate);\r
1994         calculateMenu.addSeparator();\r
1995         calculateMenu.add(pairwiseAlignmentMenuItem);\r
1996         calculateMenu.add(PCAMenuItem);\r
1997         this.add(statusBar, BorderLayout.SOUTH);\r
1998         pasteMenu.add(pasteNew);\r
1999         pasteMenu.add(pasteThis);\r
2000         sort.add(sortIDMenuItem);\r
2001         sort.add(sortByTreeMenu);\r
2002         sort.add(sortGroupMenuItem);\r
2003         sort.add(sortPairwiseMenuItem);\r
2004         calculate.add(averageDistanceTreeMenuItem);\r
2005         calculate.add(neighbourTreeMenuItem);\r
2006         calculate.add(avDistanceTreeBlosumMenuItem);\r
2007         calculate.add(njTreeBlosumMenuItem);\r
2008         helpMenu.add(documentation);\r
2009         helpMenu.add(about);\r
2010   }\r
2011 \r
2012   public void setEmbedded()\r
2013   {\r
2014 \r
2015     embeddedMenu = new Panel();\r
2016     embeddedEdit = new Label();\r
2017     embeddedSearch = new Label();\r
2018     embeddedView = new Label();\r
2019     embeddedColour = new Label();\r
2020     embeddedFile = new Label();\r
2021     embeddedHelp = new Label();\r
2022     embeddedCalculate = new Label();\r
2023     flowLayout1 = new FlowLayout();\r
2024     embeddedMenu.setBackground(Color.lightGray);\r
2025     embeddedMenu.setLayout(flowLayout1);\r
2026     embeddedEdit.setText("Edit");\r
2027     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2028     embeddedSearch.setText("Search");\r
2029     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2030     embeddedView.setText("View");\r
2031     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2032     embeddedColour.setText("Colour");\r
2033     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2034     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2035     embeddedFile.setText("File");\r
2036     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2037     embeddedHelp.setText("Help");\r
2038     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2039     embeddedCalculate.setText("Calculate");\r
2040     embeddedMenu.add(embeddedFile);\r
2041     embeddedMenu.add(embeddedEdit);\r
2042     embeddedMenu.add(embeddedSearch);\r
2043     embeddedMenu.add(embeddedView);\r
2044     embeddedMenu.add(embeddedColour);\r
2045     embeddedMenu.add(embeddedCalculate);\r
2046     embeddedMenu.add(embeddedHelp);\r
2047     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2048     flowLayout1.setHgap(2);\r
2049     flowLayout1.setVgap(0);\r
2050     embeddedFile.addMouseListener(this);\r
2051     embeddedEdit.addMouseListener(this);\r
2052     embeddedSearch.addMouseListener(this);\r
2053     embeddedView.addMouseListener(this);\r
2054     embeddedColour.addMouseListener(this);\r
2055     embeddedCalculate.addMouseListener(this);\r
2056     embeddedHelp.addMouseListener(this);\r
2057 \r
2058     setVisible(false);\r
2059     fileMenu.remove(closeMenuItem);\r
2060     fileMenu.remove(2); // Seperator\r
2061 \r
2062     applet.setLayout(new BorderLayout());\r
2063     applet.add(embeddedMenu, BorderLayout.NORTH);\r
2064     applet.add(statusBar, BorderLayout.SOUTH);\r
2065     applet.validate();\r
2066 \r
2067 \r
2068     alignPanel.setSize(applet.size().width, applet.size().height\r
2069                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2070 \r
2071      applet.add(alignPanel, BorderLayout.CENTER);\r
2072      applet.validate();\r
2073   }\r
2074 \r
2075 \r
2076 \r
2077   PopupMenu filePopup, editPopup, searchPopup,\r
2078       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2079   MenuItem featureSettings = new MenuItem();\r
2080   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2081 \r
2082   public void mousePressed(MouseEvent evt)\r
2083   {\r
2084     PopupMenu popup = null;\r
2085     Label source = (Label)evt.getSource();\r
2086     if(source==embeddedFile)\r
2087     {\r
2088       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2089     }\r
2090     else if(source==embeddedEdit)\r
2091     {\r
2092       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2093     }\r
2094     else if(source==embeddedSearch)\r
2095     {\r
2096       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2097     }\r
2098     else if(source==embeddedView)\r
2099     {\r
2100       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2101     }\r
2102     else if(source==embeddedColour)\r
2103     {\r
2104       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2105     }\r
2106     else if(source==embeddedCalculate)\r
2107     {\r
2108       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2109     }\r
2110     else if(source==embeddedHelp)\r
2111     {\r
2112       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2113     }\r
2114 \r
2115     embeddedMenu.add(popup);\r
2116     popup.show(embeddedMenu,\r
2117                source.getBounds().x,\r
2118                source.getBounds().y + source.getBounds().getSize().height);\r
2119   }\r
2120 \r
2121   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2122   {\r
2123     if(popup!=null)\r
2124     {\r
2125       return popup;\r
2126     }\r
2127     popup = new PopupMenu();\r
2128     int m, mSize = original.getItemCount();\r
2129     for(m=0; m<mSize; m++)\r
2130     {\r
2131       popup.add(original.getItem(m));\r
2132       mSize--;\r
2133       m--;\r
2134     }\r
2135 \r
2136     return popup;\r
2137   }\r
2138   public void mouseClicked(MouseEvent evt)\r
2139   {}\r
2140   public void mouseReleased(MouseEvent evt)\r
2141   {}\r
2142   public void mouseEntered(MouseEvent evt)\r
2143   {}\r
2144   public void mouseExited(MouseEvent evt)\r
2145   {}\r
2146 \r
2147 }\r
2148 \r